Re: [AMBER] How can I get a average structure?

From: Sanjib Paul <>
Date: Tue, 28 Aug 2012 21:03:41 +0530

Dear Mr.Jason,
                     I used rms command before average following TUTORIAL
B3. This time my input file was following:
trajin protein_prod_1ns.mdcrd
rms first mass .C,CA,N
average protein_prod_1ns_avg.pdb pdb
But structure is not improved. I have understood what you told me. Actually
I want a starting structure for nmode analysis which would have very small
root-mean-square gradient. I thought after getting a average structure I
would minimiza it and then that minimized structure would be starting
structure. But perhaps I was wrong. So, now how can I proceed? Please help..


On Tue, Aug 28, 2012 at 7:43 PM, Jason Swails <>wrote:

> On Tue, Aug 28, 2012 at 10:05 AM, Sanjib Paul <
> >wrote:
> > Dear Amber Users,
> > I wanted to generate a average structure
> form 1
> > ns trajectory file of my protein using 'average' command of ptraj. My
> input
> > file is like following:
> > trajin protein_prod_1ns.mdcrd
> > average protein_prod_1ns_avg.pdb pdb
> >
> Note, the 'average' command does not do any kind of implicit fitting, so
> you are including free rotation and translation in your average (which is
> *NOT* something you probably want to do).
> To get rid of these contributions, add a "rms" command before 'average'.
> > When I observe my pdb file of average structure I noticed that some
> portion
> > of protein is very unstable and very absurd. Atoms are overlapping and
> some
> > unusual bonds are also present. Then, I followed analysis portion of
> > TUTORIAL B3. Here also structure is like before. Some unusual bonds and
> > overlapped atoms are present. How can I overcome it? Please help.
> >
> 'Warped' and 'strange' structures are expected for an average (to some
> extent). Consider for instance a freely rotating methyl group such that
> all hydrogens attached to the CH3 are rotationally degenerate. In this
> case, each hydrogen atom should have the *same* average coordinates which
> should lie almost directly on top of the C atom they are all attached to.
> You should think about what you really want and whether or not an 'average'
> structure satisfies your needs.
> HTH,
> Jason
> --
> Jason M. Swails
> Quantum Theory Project,
> University of Florida
> Ph.D. Candidate
> 352-392-4032
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Received on Tue Aug 28 2012 - 09:00:02 PDT
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